                                                     (:largest-seen (:linear-index idx-status)))}
                      :no-coordinate-alns no-coordinate-alns))))
 
-(defn- make-index
+(defn make-index
   [refs alns]
   (merge
    (zipmap (map :name refs)

      :bin-index    (update-bin-index bin-index aln)
      :linear-index (update-linear-index linear-index aln))))

(defn- make-index!
  [refs alns]
  (loop [[aln & rest] alns
         ref-name (:rname aln)

            [cljam.util :refer [gen-vec]]
            [cljam.util.sam-util :as sam-util]
            [cljam.util.bgzf-util :as bgzf-util]
            [cljam.bam-index.common :refer :all]
            [cljam.bam-index.chunk :as chunk])
  (:import [java.io DataOutputStream FileOutputStream Closeable]))

(defn- find-ref
